KEY TASK Develop a work plan to achieve Goals

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5 Strategic Direction 2: A tool box for tomorrow focused on ensuring our biosecurity system harnesses science and technology to transform the way we do biosecurity KEY TASK Develop a work plan to achieve Goals

6 Goal 1 The best science underpins biosecurity Science & Innovation Strategy with Implementation Plan Best science; international; cross discipline; funding Goal 2 Current tools - continuous improvement More effective, safe, and socially accepted tools; KM/MM are core Goal 3 New tools capitalising on innovation and technology Collaboration; pipeline; inexpensive and effective Wide participation; legislation, regulations help drive participation

7 Goal 1 The best science outcomes: Science uptake, relevant, timely, and effective Goal 2 Current tools outcomes: More effective use of existing tools Application of existing technologies to enhance tools Social licence to allow the use of existing tools Goal 3 New tools outcomes: Tools for workers Tools for participation Tools for monitoring and analysis

8 Development of a Statement of RS&T Priorities Developing and communicating an integrated Biosecurity Science Plan (BSP) Establish a mechanism to regularly review and update the BSP Strengthen science collaboration through establishing and resourcing a mechanism Identify critical social licence issues /facilitate engagement Develop tools to support effective and faster decision-making Ensure tool development has strong stakeholder engagement

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10 Enhancing surveillance capabilities: Building a partnership Steve Pawson, Andrea Grant, Rebecca Turner, Eckehard Brockerhoff (Scion) Jon Sullivan Melanie Mark-Shadbolt (Lincoln University) March 2018

11 Continuous improvement of current biosecurity tools

12 Transformational new tools

13 Using biosecurity data to inform public surveillance activities Use existing data, e.g., interceptions Models to identify trends and specific threats Provide alerts through to users of the community. Rebecca Turner

14 Will people use new tools?

15 Myrtle rust reporter Launched in November 2017 Involves people in recording and identifying host plants and reporting myrtle rust active installs Sixty six reporters over 270 records Eight reports of myrtle rust Generates a strong visible engagement between the MPI response and the public

16 Myrtle rust reporter

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19 Molecular Tools in Tomorrows Toolbox Rebecca McDougal

20 Tomorrow s Toolbox Goals Biosecurity The best science underpins our biosecurity system 2. Continuous improvement of current biosecurity tools value from current tools 3. New Tools innovation and technology, proactively seeking out transformational tools Molecular (DNA-based) tools for diagnostics & biosecurity contribute significantly to these goals

21 1. The best science underpins our biosecurity system Genomics: whole genome sequencing of pathogens Understanding pathogen diversity e.g. Phytophthora pluvialis two types (Brar, et al. 2017) Others: P. kernoviae, P. cactorum Eucalyptus Variegated Beetle (not whole genomes) Functional gene analyses e.g. effectors Metagenomics & Metabarcoding for setting the baseline what is present already? Should we move away from traditional taxonomy-based biosecurity that relies on names towards identifying a pathogenic trait or gene (identify potential risk)? (McTaggart et al. 2016)

22 2. Continuous improvement of current biosecurity tools PCR advances: extreme PCR (15-60s!), throughput becomes irrelevant. Portable DNA amplification: RPA, LAMP, portable devices Real-time monitoring of airbourne pathogen spores for disease risk alerts: Spore traps, with automated spore lysis, DNA amplification, quantification and remote reporting incl. climatic data. Can be integrated with infection models and risk predictions sent to users J. West, Rothamsted. Metagenomics & Meta-barcoding - complex samples & unculturable pathogens Using rooftop spore traps (on cars or buildings!) soup of DNA from all sorts of organisms NGS and/or species-specific detection (PCR) Nicolaisen, West, et al. 2017

23 3. New Tools innovation and technology in-field genome sequencing MinION e.g. disease diagnostics for Zika & Ebola, identification of closely related plant-species. Digital droplet PCR - has been used in soil microbiology effectively e.g. detection of bacteria and viruses low inhibition by soil inhibitors absolute quantification of targets Chip-based microarrays for microbial community structure & interactions, incl. functional genes massively high-throughput (140,000 probes) and quantitative e.g. GeoChip GeoChip He et al Biosensors for pathogen detection: VOCs and whole pathogen spore DNA-aptamer based biosensors ( Pikorua of Protection MBIE bid, Tara & Brian) Brooke O Connor

24 Summary Exciting research that underpins potential new tools for biosecurity toolbox Genomics, population/genetic diversity studies, metagenomics The tools the we currently use are continually under improvement PCR & isothermal methods, spore-trapping undergoing major shifts for pest detection New Tools also being developed, or applied to biosecurity that have been used in different context i.e. clinical/human diagnostics, food microbiology Digital droplet PCR, MinION and Biosensors = exciting tools in development now Overall trend diagnostics on-site, will we still need lab-based verification? will enable early detection Diagnostics-in-a-Suitcase Plant Biosecurity CRC

25 Rebecca McDougal Molecular Forest Pathologist Date: 15 March 2018

26 New Genetics for New Challenges Emily Telfer

27 Challenges Biosecurity 2025 Challenges of the future are not the disease and pests we know about, but the ones that may: ARRIVE in shipping containers, or in the case of myrtle rust purportedly on a Cyclone. ARISE like KDB that appears to have been here for several hundred years and may have activated by climate change or human activity

28 Tomorrow s Toolbox Biosecurity 2025 You can t beat good breeding Getting by with a little help from your friends Age is just a number If in doubt, edit it out.. or in

29 Genomic-enhanced breeding plans Breeding programmes will continue to be the mainstay of long-term resilience to disease and improved characteristics Selection with DNA markers will speed up the delivery of genetic gains 21 years to 7 years in radiata pine.. 15 years to 4 years in eucalypts Identity by state genomic reconstructed pedigrees reveal hidden relatedness and avoid inbred populations Breeding by design to pyramid multiple traits Identification of causative variants

30 Protective Microbiomes Microbiome in relationship with host species can have benefits. Development of selection of individuals based on the Endo-biome profile Kiwifruit Metabarcoding Profiles a new quantitative trait Sheep High-throughput microbial profiling Radiata Molecular signatures of tolerance to red needle cast in Pinus radiata Infiltration of tissue culture lines with beneficial microbes could vaccinate trees and improve over-all fitness Douglas-fir Increased Biomass of Nursery-Grown Seedlings upon Inoculation with Diazotrophic Endophytic Consortia

31 Epigenetics Epigenetic remodelling throughout the lifetime of a plant Developmental changes Environmental changes Adaptive potential Maturation & Aging Methylation impacts gene expression CpG Topical micrornas Gene silencing Systemic Acquired Resistance - SARs Activated suite of defence genes

32 Gene editing Cas9/CRISPR gene editing Homology directed repair (HDR) using a template Introduce very targeted changes into elite material edit correlation breakers Finding causal regulatory variants is hard Specific resistance genes Specific SNP variants that are rare in a population Increase the prevalence in a population Promotion of Alleles by Genome Editing

33 Tomorrow s Toolbox Biosecurity 2025 Breeding programmes You can t beat good breeding Foundation of biosecurity Microbiomes Getting by with a little help from your friends Inherited and Induced endophytes Epigenetics effects Age is just a number Genome remodelling Gene Editing If in doubt, edit it out. or in Targeted variants in already improved population

34 Emily Telfer Quantitative & Molecular Genetics Leader Date: 15 March 2018